Variants of SARS-CoV-2

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Positive, negative, and neutral mutations during the evolution of coronaviruses like SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has a lot of variants. Some of them are important because of increased transmission and vaccines being less effective on them.[1][2] This article discusses relevant variants of SARS-CoV-2 and mutations in these variants.

The variant WIV04/2019 is most closely related to the original virus when it began infecting humans.[3]

Overview[change | change source]

There are a lot of lineages of SARS-CoV-2.[4] Lineages are variants that are genetically the same.

Nomenclature[change | change source]

SARS-CoV-2 corresponding nomenclatures[5]
PANGO lineages[6] Notes to PANGO lineages[7] Nextstrain clades,[8] 2021[9] GISAID clades Notable variants
A.1–A.6 19B S contains "reference sequence" WIV04/2019[3]
B.3–B.7, B.9, B.10, B.13–B.16 19A L
B.2 V
B.1 B.1.5–B.1.72 20A G Lineage B.1 in the PANGO Lineages nomenclature system
B.1.9, B.1.13, B.1.22, B.1.26, B.1.37 GH
B.1.3–B.1.66 20C Includes Lineage B.1.429 / CAL.20C[10] and Lineage B.1.525[11]
20G Predominant in US generally, Jan '21[10]
20H Includes B.1.351 aka 20H/501Y.V2 or 501.V2 lineage
B.1.1 20B GR Includes B.1.1.207[source?]
20J Includes P.1 and P.2[12][13]
20I Includes lineage B.1.1.7 aka VOC-202012/01, VOC-20DEC-01 or 20I/501Y.V1
B.1.177 20E (EU1)[9] GV[a] Derived from 20A[9]

There's no consistent nomenclature for SARS-CoV-2.[15] Variants are usually refered to by the country where the variant came from.[16][17][18] For example, B.1.1.7 is usually called the "UK variant."

Criteria for importance[change | change source]

Viruses generally mutate over time, creating new variants. When a new variant grows in a population, it's labeled as an "emerging variant".

Some of the potential consequences of emerging variants are the following:[19][20]

  • Increased transmissibility
  • Increased Morality (death).
  • Ability to evade natural immunity (e.g., causing reinfections)
  • Ability to infect vaccinated people

Notable variants[change | change source]

Cluster 5[change | change source]

In early November 2020, Cluster 5, also referred to as ΔFVI-spike by the Danish State Serum Institute (SSI),[21] was discovered in Northern Jutland, Denmark, and is believed to have been spread from minks to humans via mink farms. On 4 November 2020, it was announced that the mink population in Denmark would be culled to prevent the possible spread of this mutation and reduce the risk of new mutations happening. A lockdown and travel restrictions were introduced in seven municipalities of Northern Jutland to prevent the mutation from spreading, which could compromise national or international responses to the COVID-19 pandemic. By 5 November 2020, some 214 mink-related human cases had been detected.[22]

The World Health Organization (WHO) has stated that cluster 5 has a "moderately decreased sensitivity to neutralizing antibodies".[23] SSI warned that the mutation could reduce the effect of COVID-19 vaccines under development, although it was unlikely to render them useless. Following the lockdown and mass-testing, SSI announced on 19 November 2020 that cluster 5 in all probability had become extinct.[24] As of 1 February 2021, authors to a peer-reviewed paper, all of whom were from the SSI, assessed that cluster 5 was not in circulation in the human population.[25]

Lineage B.1.1.7 / Variant of Concern 20DEC-01[change | change source]

False-colour transmission electron micrograph of a B.1.1.7 variant coronavirus. The variant's increased transmissibility is believed to be due to changes in structure of the spike proteins, shown here in green.

This variant was first detected in October 2020 during the COVID-19 pandemic in the United Kingdom from a sample taken the month before in Kent.[26] Lineage B.1.1.7,[27] It's correlated with a big increase in COVID-19 infection in United Kingdom, partly because of the N501Y mutation.[28] There is some evidence that this variant has 40%–80% increased transmissibility and an increase in deadliness.[29][30]

Variant of Concern 21FEB-02[change | change source]

Variant of Concern 21FEB-02 (previously written as VOC-202102/02), described by Public Health England (PHE) as "B.1.1.7 with E484K"[31] is the B.1.1.7 variant with an additional E484K mutation. As of 17 March 2021, there are 39 confirmed cases of VOC-21FEB-02 in the UK.[31] On 4 March 2021, scientists reported B.1.1.7 with E484K mutations in the state of Oregon. It seems that this combination happened randomly in Oregon, instead of coming from the UK.

Lineage B.1.1.317[change | change source]

B.1.1.317 is not a variant of concern, but Queensland Health forced 2 people in hotel quarantine in Brisbane, Australia to go through an extra 5 days quarantine on top of the mandatory 14 days after it was confirmed they were infected with this variant.[32]

Lineage B.1.1.318[change | change source]

Lineage B.1.1.318 was detected on 24 February 2021. 16 cases of it have been detected in the UK.[31][33]

Lineage B.1.351[change | change source]

On 18 December 2020, the 501.V2 variant, also known as 501.V2, 20H/501Y.V2 (formerly 20C/501Y.V2), VOC-20DEC-02 (formerly VOC-202012/02), or lineage B.1.351,[19] was first detected in South Africa and reported by the country's health department.[34] Researchers and officials reported that the variant is more likely to make young people very sick.[35][36] The South African health department also said that the variant may be driving the second wave of the COVID-19 epidemic in the country.[34][35]

Scientists said that the variant has many mutations that allow it to attach more easily to human cells because of the following three mutations in the receptor-binding domain (RBD) in the spike glycoprotein of the virus: N501Y,[34][37] K417N, and E484K.[38][39] The N501Y mutation has also been detected in the United Kingdom.[34][40]

Lineage B.1.429 / CAL.20C[change | change source]

Lineage B.1.429, also known as CAL.20C, has by five distinct mutations (I4205V and D1183Y in the ORF1ab-gene, and S13I, W152C, L452R in the spike proteins S-gene).[10][41] B.1.429 might be more transmissible.[41] The CDC has listed B.1.429 and the related B.1.427 as "variants of concern," and says that they have a ~20% increase in transmissibility.

B.1.429 was first discovered in July 2020 by researchers at the Cedars-Sinai Medical Center, California, in one of 1,230 virus samples collected in Los Angeles County since the start of the COVID-19 epidemic.[42] It wasn't detected again until September when it reappeared among samples in California, but numbers remained very low until November.[43][44] In November 2020, the CAL.20C variant accounted for 36 percent of samples collected at Cedars-Sinai Medical Center, and by January 2021, the CAL.20C variant was 50 percent of samples.[41]

Lineage B.1.525[change | change source]

B.1.525, also called VUI-21FEB-03[31] (previously VUI-202102/03) by Public Health England (PHE) and formerly known as UK1188,[31] doesn't have the same N501Y mutation found in B.1.1.7, 501.V2 and P.1, but has the same E484K-mutation as found in the P.1, P.2, and 501.V2 variants.[45] B.1.525 is different from all other variants by having both the E484K-mutation and a new F888L mutation. As of March 5, it had been found in 23 countries, including the UK, Denmark, Finland, Norway, Netherlands, Belgium, France, Spain, Nigeria, Ghana, Jordan, Japan, Singapore, Australia, Canada, Germany, Italy, Slovenia, Austria, Malaysia, Switzerland, the Republic of Ireland and the US.[46][47][48][49][50][51][52]

Lineage P.1[change | change source]

Lineage P.1, termed Variant of Concern 21JAN-02[31] (formerly VOC-202101/02) by Public Health England[31] and 20J/501Y.V3 by Nextstrain,[11] was found in Tokyo on 6 January 2021 by the National Institute of Infectious Diseases (NIID). The new lineage was first identified in four people who arrived in Tokyo having travelled from the Brazilian Amazonas state on 2 January 2021.[53] On 12 January 2021, the Brazil-UK CADDE Centre confirmed 13 local cases of the P.1 new lineage in the Amazon rain forest.[54] This variant of SARS-CoV-2 has been named P.1 lineage (although it is a descendant of B.1.1.28, the name B. is not permitted and thus the resultant name is P.1), and has 17 unique amino acid changes, 10 of which in its spike protein, including the three concerning mutations: N501Y, E484K and K417T.[54][55][56][57]

A study of samples from Manaus between November 2020 and January 2021, showed the P.1 lineage to be 1.4–2.2 times more transmissible. The variant is also 10–80% more deadly.[58][59][60]

A vaccinated person has a higher risk of getting a mild P.1 infection while still being 100% protected against hospitalisation or death.[61]

Preliminary data from two studies indicate that the Oxford–AstraZeneca vaccine is effective against the P.1 variant, although the exact level of efficacy has not yet been released.[62][63] Preliminary data from a study conducted by Instituto Butantan suggest that CoronaVac is effective against the P.1 variant as well, and the study will be expanded to obtain definitive data.[64]

Differential vaccine effectiveness[change | change source]

Notes[change | change source]

  1. 1.0 1.1 In another source, GISAID name a set of 7 clades without the O clade but including a GV clade.[14]

References[change | change source]

  1. "Coronavirus variants and mutations: The science explained". BBC News. 6 January 2021. Retrieved 2 February 2021.
  2. Kupferschmidt, Kai (15 January 2021). "New coronavirus variants could cause more reinfections, require updated vaccines". Science. American Association for the Advancement of Science. doi:10.1126/science.abg6028. S2CID 234141081. Retrieved 2 February 2021.
  3. 3.0 3.1 Zhukova, Anna; Blassel, Luc; Lemoine, Frédéric; Morel, Marie; Voznica, Jakub; Gascuel, Olivier (24 November 2020). "Origin, evolution and global spread of SARS-CoV-2". Comptes Rendus Biologies. 344: 57–75. doi:10.5802/crbiol.29. PMID 33274614.
  4. "Lineage descriptions". Pango team.
  5. This table is an adaptation and expansion of Alm et al., figure 1.
  6. Rambaut, A.; Holmes, E.C.; O’Toole, Á.; et al. (2020). "A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology". Nature Microbiology. 5 (11): 1403–1407. doi:10.1038/s41564-020-0770-5. PMC 7610519. PMID 32669681. S2CID 220544096. Cited in Alm et al.
  7. Alm, E.; Broberg, E. K.; Connor, T.; Hodcroft, E. B.; Komissarov, A. B.; Maurer-Stroh, S.; et al. (2020). "Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020". Euro Surveillance. 25 (32). doi:10.2807/1560-7917.ES.2020.25.32.2001410. PMC 7427299. PMID 32794443.
  8. "Nextclade". Archived from the original (What are the clades?) on 19 January 2021. Retrieved 19 January 2021.
  9. 9.0 9.1 9.2 Bedford, Trevor; Hodcroft, Emma B; Neher, Richard A (6 January 2021). "Updated Nextstrain SARS-CoV-2 clade naming strategy". Retrieved 19 January 2021.
  10. 10.0 10.1 10.2 Zhang, Wenjuan; Davis, Brian D.; Chen, Stephanie S.; Martinez, Jorge M Sincuir; Plummer, Jasmine T.; Vail, Eric (2021). "Emergence of a novel SARS-CoV-2 strain in Southern California, USA". doi:10.1101/2021.01.18.21249786. S2CID 231646931. {{cite journal}}: Cite journal requires |journal= (help)
  11. 11.0 11.1 "SARS-CoV-2 Variant Classifications and Definitions". Centers for Disease Control and Prevention. 11 February 2020.
  12. "PANGO lineages-Lineage B.1.1.28". Retrieved 4 February 2021.[not in the source given]
  13. "Variant: 20J/501Y.V3". 1 April 2021. Retrieved 6 April 2021.
  14. "clade tree (from 'Clade and lineage nomenclature')". 4 July 2020. Retrieved 7 January 2021.
  15. WHO Headquarters (8 January 2021). "3.6 Considerations for virus naming and nomenclature". SARS-CoV-2 genomic sequencing for public health goals: Interim guidance, 8 January 2021. World Health Organization. p. 6. Retrieved 2 February 2021.
  16. "Don't call it the 'British variant.' Use the correct name: B.1.1.7". STAT. 9 February 2021. Retrieved 12 February 2021.
  17. Flanagan, Ryan (2 February 2021). "Why the WHO won't call it the 'U.K. variant', and you shouldn't either". Coronavirus. Retrieved 12 February 2021.
  18. For a list of sources using names referring to the country in which the variants were first identified, see, for example, Talk:South African COVID variant and Talk:U.K. Coronavirus variant.
  19. 19.0 19.1 "Emerging SARS-CoV-2 Variants". (Science brief). Centers for Disease Control and Prevention. 28 January 2021. Retrieved 4 January 2021. This article incorporates text from this source, which is in the public domain.
  20. "COVID "Mega-variant" and eight criteria for a template to assess all variants". Science Speaks: Global ID News. 2 February 2021. Retrieved 20 February 2021.
  21. Lassaunière, Ria; Fonager, Jannik; Rasmussen, Morten; Frische, Anders; Strandh, Charlotta; Rasmussen, Thomas; et al. (10 November 2020). SARS-CoV-2 spike mutations arising in Danish mink, their spread to humans and neutralization data (Preprint). Statens Serum Institut. Archived from the original on 10 November 2020. Retrieved 11 November 2020.
  22. "Detection of new SARS-CoV-2 variants related to mink" (PDF). European Centre for Disease Prevention and Control. 12 November 2020. Retrieved 12 November 2020.
  23. "SARS-CoV-2 mink-associated variant strain – Denmark". WHO Disease Outbreak News. 6 November 2020. Archived from the original on 12 November 2020. Retrieved 19 March 2021.
  24. Kevany S, Carstensen T (19 November 2020). "Danish Covid mink variant 'very likely extinct', but controversial cull continues". The Guardian. Archived from the original on 24 April 2021. Retrieved 19 April 2021.
  25. Larsen, Helle Daugaard; Fonager, Jannik; Lomholt, Frederikke Kristensen; Dalby, Tine; Benedetti, Guido; Kristensen, Brian; Urth, Tinna Ravnholt; Rasmussen, Morten; Lassaunière, Ria; Rasmussen, Thomas Bruun; Strandbygaard, Bertel (4 February 2021). "Preliminary report of an outbreak of SARS-CoV-2 in mink and mink farmers associated with community spread, Denmark, June to November 2020". Eurosurveillance. 26 (5). doi:10.2807/1560-7917.ES.2021.26.5.210009. ISSN 1025-496X. PMC 7863232. PMID 33541485.
  26. "Covid: Ireland, Italy, Belgium and Netherlands ban flights from UK". BBC News. 20 December 2020.
  27. Chand, Meera; Hopkins, Susan; Dabrera, Gavin; Achison, Christina; Barclay, Wendy; Ferguson, Neil; Volz, Erik; Loman, Nick; Rambaut, Andrew; Barrett, Jeff (21 December 2020). Investigation of novel SARS-COV-2 variant: Variant of Concern 202012/01 (PDF) (Report). Public Health England. Retrieved 23 December 2020.
  28. "New evidence on VUI-202012/01 and review of the public health risk assessment". Retrieved 4 January 2021.
  29. Gallagher, James (22 January 2021). "Coronavirus: UK variant 'may be more deadly'". BBC News. Retrieved 22 January 2021.
  30. Peter Horby; Catherine Huntley; Nick Davies; Edmunds; Neil Ferguson; Graham Medley; Andrew Hayward; Muge Cevik; Calum Semple (11 February 2021). "NERVTAG paper on COVID-19 variant of concern B.1.1.7: NERVTAG update note on B.1.1.7 severity (2021-02-11)" (PDF).
  31. 31.0 31.1 31.2 31.3 31.4 31.5 31.6 "Variants: distribution of cases data". Government Digital Service.
  32. "Queensland travellers have hotel quarantine extended after Russian variant of coronavirus detected". 3 March 2021. Retrieved 3 March 2021.
  33. "Latest update: New Variant Under Investigation designated in the UK". 4 March 2021. Retrieved 5 March 2021.
  34. 34.0 34.1 34.2 34.3 "South Africa announces a new coronavirus variant". The New York Times. 18 December 2020. Retrieved 20 December 2020.
  35. 35.0 35.1 Wroughton, Lesley; Bearak, Max (18 December 2020). "South Africa coronavirus: Second wave fueled by new strain, teen 'rage festivals'". The Washington Post. Retrieved 20 December 2020.
  36. Mkhize, Dr Zwelini (18 December 2020). "Update on Covid-19 (18th December 2020)" (Press release). South Africa. COVID-19 South African Online Portal. Retrieved 23 December 2020. Our clinicians have also warned us that things have changed and that younger, previously healthy people are now becoming very sick.
  37. Abdool Karim, Salim S. (19 December 2020). "The 2nd Covid-19 wave in South Africa:Transmissibility & a 501.V2 variant, 11th slide".
  38. Lowe, Derek (22 December 2020). "The New Mutations". In the Pipeline. American Association for the Advancement of Science. Archived from the original on 29 January 2021. Retrieved 23 December 2020. I should note here that there's another strain in South Africa that is bringing on similar concerns. This one has eight mutations in the Spike protein, with three of them (K417N, E484K and N501Y) that may have some functional role.
  39. "Statement of the WHO Working Group on COVID-19 Animal Models (WHO-COM) about the UK and South African SARS-CoV-2 new variants" (PDF). World Health Organization. 22 December 2020. Retrieved 23 December 2020.
  40. "Novel mutation combination in spike receptor binding site" (Press release). GISAID. 21 December 2020. Archived from the original on 22 February 2021. Retrieved 23 December 2020.
  41. 41.0 41.1 41.2 "New California Variant May Be Driving Virus Surge There, Study Suggests". New York Times. 19 January 2021.
  42. "Local COVID-19 Strain Found in Over One-Third of Los Angeles Patients". news wise (Press release). California: Cedars Sinai Medical Center. 19 January 2021. Retrieved 3 March 2021.
  43. "B.1.429". Rambaut Group, University of Edinburgh. PANGO Lineages. 15 February 2021. Retrieved 16 February 2021.
  44. "B.1.429 Lineage Report". Scripps Research. 15 February 2021. Retrieved 16 February 2021.
  45. "Delta-PCR-testen" [The Delta PCR Test] (in Danish). Statens Serum Institut. 25 February 2021. Retrieved 27 February 2021.
  46. "GISAID hCOV19 Variants (see menu option 'G/484K.V3 (B.1.525)')". Retrieved 4 March 2021.
  47. "Status for udvikling af SARS-CoV-2 Variants of Concern (VOC) i Danmark" [Status of development of SARS-CoV-2 Variants of Concern (VOC) in Denmark] (in Danish). Statens Serum Institut. 27 February 2021. Retrieved 27 February 2021.
  48. "Varianten van het coronavirus SARS-CoV-2" [Variants of the coronavirus SARS-CoV-2] (in Dutch). Rijksinstituut voor Volksgezondheid en Milieu, RIVM. 16 February 2021. Retrieved 16 February 2021.
  49. "B.1.525". Pango team. Retrieved 22 March 2021.
  50. "A coronavirus variant with a mutation that 'likely helps it escape' antibodies is already in at least 11 countries, including the US". Business Insider. 16 February 2021. Retrieved 16 February 2021.
  51. "En ny variant av koronaviruset er oppdaget i Norge. Hva vet vi om den?" [A new variant of the coronavirus has been discovered in Norway. What do we know about it?] (in Norwegian). Aftenposten. 18 February 2021. Retrieved 18 February 2021.
  52. Cullen, Paul (25 February 2021). "Coronavirus: Variant discovered in UK and Nigeria found in State for first time". The Irish Times. Retrieved 25 February 2021. Gataveckaite, Gabija (25 February 2021). "First Irish case of B1525 strain of Covid-19 confirmed as R number increases". Irish Independent. Retrieved 25 February 2021. McGlynn, Michelle (25 February 2021). "Nphet confirm new variant B1525 detected in Ireland as 35 deaths and 613 cases confirmed". Irish Examiner. Retrieved 25 February 2021.
  53. "Japan finds new coronavirus variant in travelers from Brazil". Japan Today. Japan. 11 January 2021. Retrieved 14 January 2021.
  54. 54.0 54.1 Faria, Nuno; Claro, Ingra; Candido, Darlan; Franco, Lucas; Andrade, Pamela; Coletti, Thais; et al. (12 January 2021). "Genomic characterisation of an emergent SARS-CoV-2 lineage in Manaus: preliminary findings". CADDE Genomic Network. Retrieved 23 January 2021.
  55. Covid-19 Genomics UK Consortium (15 January 2021). "COG-UK Report on SARS-CoV-2 Spike mutations of interest in the UK" (PDF). Retrieved 25 January 2021.
  56. "P.1 report". Retrieved 8 February 2021.
  57. Voloch, Carolina M.; F, Ronaldo da Silva; Almeida, Luiz G. P. de; Cardoso, Cynthia C.; Brustolini, Otavio J.; Gerber, Alexandra L.; Guimarães, Ana Paula de C.; Mariani, Diana; Costa, Raissa Mirella da; Ferreira, Orlando C.; Workgroup, Covid19-UFRJ (2020). "Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil, Figure 5". doi:10.1101/2020.12.23.20248598. S2CID 229379623. Retrieved 15 January 2021 – via MedRxiv. {{cite journal}}: Cite journal requires |journal= (help)
  58. Andreoni, Manuela; Londoño, Ernesto; Casado, Leticia (3 March 2021). "Brazil's Covid Crisis Is a Warning to the Whole World, Scientists Say – Brazil is seeing a record number of deaths, and the spread of a more contagious coronavirus variant that may cause reinfection". The New York Times. Retrieved 3 March 2021.
  59. Zimmer, Carl (1 March 2021). "Virus Variant in Brazil Infected Many Who Had Already Recovered From Covid-19 – The first detailed studies of the so-called P.1 variant show how it devastated a Brazilian city. Now scientists want to know what it will do elsewhere". The New York Times. Retrieved 3 March 2021.
  60. Faria, Nuno; Mellan, Thomas; Whittaker, Charles; Claro, Ingra; Candido, Darlan; Mishra, Swapnil; et al. (3 March 2021). "Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil". medRxiv : The Preprint Server for Health Sciences (Preprint). doi:10.1101/2021.02.26.21252554. PMC 7941639. PMID 33688664. Retrieved 23 March 2021 – via medRxiv. P.1 can be between 1.4-2.2 (50% BCI, with a 96% posterior probability of being >1) times more transmissible than local non-P1 lineages ... We estimate that infections are 1.1–1.8 (50% BCI, 81% posterior probability of being >1) times more likely to result in mortality in the period following P.1's emergence, compared to before, although posterior estimates of this relative risk are also correlated with inferred cross-immunity
  61. Garcia-Beltran, Wilfredo; Lam, Evan; Denis, Kerri (18 February 2021). "Circulating SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity". doi:10.1101/2021.02.14.21251704. Retrieved 3 March 2021 – via medrxiv.
  62. Gaier, Rodrigo (5 March 2021). "Exclusive: Oxford study indicates AstraZeneca effective against Brazil variant, source says". Reuters. Rio de Janeiro. Retrieved 9 March 2021.
  63. "Exclusive: Oxford study indicates AstraZeneca effective against Brazil variant, source says". Reuters. Rio de Janeiro. 8 March 2021. Retrieved 9 March 2021.
  64. Simões, Eduardo; Gaier, Rodrigo (8 March 2021). "CoronaVac e Oxford são eficazes contra variante de Manaus, dizem laboratórios" [CoronaVac and Oxford are effective against Manaus variant, say laboratories]. UOL Notícias (in Portuguese). Reuters Brazil. Retrieved 9 March 2021.

Other websites[change | change source]